8-37604901-A-G

Variant names:

• chr8-37604901-A-G
• rs1573266
• ENST00000517714.1:n.136-1482T>C

Variant summary

Our verdict is Benign. The variant received -12 ACMG points: 0P and 12B. BP4_Strong BA1

The ENST00000517714.1(LINC01605):​n.136-1482T>C variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.526 in 151,982 control chromosomes in the GnomAD database, including 21,188 homozygotes. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: 𝑓 0.53 (21188 hom., cov: 32)
• Consequence: LINC01605 ENST00000517714.1 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: 0.230
• Publications: 8 publications found

Genes affected

LINC01605 (HGNC:51654): (long intergenic non-protein coding RNA 1605)

LOC105379380 (HGNC:):

ACMG classification

Our verdict: Benign. The variant received -12 ACMG points.

• BP4: Computational evidence support a benign effect (BayesDel_noAF=-0.95).
• BA1: GnomAd4 highest subpopulation (EAS) allele frequency at 95% confidence interval = 0.545 is higher than 0.05.

Variant Effect in Transcripts

ACMG analysis was done for transcript: ENST00000517714.1. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
There are no transcript annotations for this variant.

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	LINC01605	ENST00000517714.1	TSL:4	n.136-1482T>C		intron	N/A
	LINC01605	ENST00000784043.1		n.250-1482T>C		intron	N/A
	LINC01605	ENST00000784117.1		n.248-1482T>C		intron	N/A

Frequencies

GnomAD3 genomes AF: 0.526 AC: 79825 AN: 151862 Hom.: 21153 Cov.: 32

Gnomad AFR AF: 0.470

Gnomad AMI AF: 0.553

Gnomad AMR AF: 0.531

Gnomad ASJ AF: 0.457

Gnomad EAS AF: 0.562

Gnomad SAS AF: 0.544

Gnomad FIN AF: 0.586

Gnomad MID AF: 0.462

Gnomad NFE AF: 0.548

Gnomad OTH AF: 0.517

We have no GnomAD4 exomes data on this position. Probably position not covered by the project.

GnomAD4 genome AF: 0.526 AC: 79916 AN: 151982 Hom.: 21188 Cov.: 32 AF XY: 0.530 AC XY: 39383 AN XY: 74278

African (AFR) AF: 0.471 AC: 19517 AN: 41452

American (AMR) AF: 0.532 AC: 8127 AN: 15290

Ashkenazi Jewish (ASJ) AF: 0.457 AC: 1586 AN: 3472

East Asian (EAS) AF: 0.562 AC: 2884 AN: 5132

South Asian (SAS) AF: 0.545 AC: 2618 AN: 4808

European-Finnish (FIN) AF: 0.586 AC: 6195 AN: 10570

Middle Eastern (MID) AF: 0.469 AC: 138 AN: 294

European-Non Finnish (NFE) AF: 0.548 AC: 37250 AN: 67940

Other (OTH) AF: 0.519 AC: 1097 AN: 2112

Alfa AF: 0.540 Hom.: 48194

Bravo AF: 0.519

Asia WGS AF: 0.551 AC: 1913 AN: 3478

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
BayesDel_noAF	Benign	-0.95
CADD	Benign	5.0
DANN	Benign	0.61
PhyloP100		0.23

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

dbSNP: rs1573266;

hg19: chr8-37462419;